Puella Magi Madoka Magica has a lot of hidden buddhist motifs and symbolisms. There's even a published book on Amazon analyzing how buddhist ideas show up in the anime.
I would say that all the dark magical girls since 2011 have been influenced by Madoka Magica - Yuki Yuna, Mahou Shoujo Site, Magical Girl Raising Project and Magical Girl Spec-Ops Asuka as the best known. In addition, there are also some magical girls with a more adult theme, even though they are not so dark, such as Flip Flappers and Machikado Mazoku. I would also add some stories that are not strictly in the genre of magical girls, such as Qualia the Purple and Wonder Egg Priority.
It is also worth noting that there are at least two books in English to seriously discuss and analyze the themes of Madoka Magica: "The Very Soil: An Unauthorized Critical Study of Puella Magi Madoka Magica" and "Revelations: An In-Depth Look at the Themes and Symbols of Puella Magi Madoka Magica". I don't know if there is anything like that for other magical girl anime - at Amazon, at least, I never found anything.
https://www.youtube.com/watch?v=i9nUqUzWDIs
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This was a fun video on another point of view <3!
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This was an amazing book that open my eyes and help me truly understand the view point of his work. <3
Here's something you might find relevant to what you're looking for. I found this while looking around Amazon to see what manga spinoff volumes were available. Also, you might want something like this if you want to see some of what went into the production of the series.